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Kraus A, Spät P, Timm S, Wilson A, Schumann R, Hagemann M, Maček B, Hess WR. Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria. Nat Commun 2024; 15:1911. [PMID: 38429292 PMCID: PMC10907346 DOI: 10.1038/s41467-024-46253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.
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Affiliation(s)
- Alexander Kraus
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Philipp Spät
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Stefan Timm
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Amy Wilson
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Rhena Schumann
- Biological Station Zingst, University of Rostock, D-18374, Zingst, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany.
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Zhou J, Qin W, Lu X, Yang Y, Stahl D, Jiao N, Zhou J, Liu J, Tu Q. The diversity and ecological significance of microbial traits potentially involved in B 12 biosynthesis in the global ocean. MLIFE 2023; 2:416-427. [PMID: 38818271 PMCID: PMC10989127 DOI: 10.1002/mlf2.12095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/21/2023] [Accepted: 10/04/2023] [Indexed: 06/01/2024]
Abstract
Cobalamin (B12), an essential nutrient and growth cofactor for many living organisms on Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related to B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomic make-up of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and the taxa harboring them in the global ocean, despite the limitations of detecting de novo B12 synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth, differentiating the epipelagic zones from the mesopelagic layers. Functional genes related to B12 biosynthesis were relatively stably distributed across different oceans, but the taxa harboring them varied considerably, showing clear functional redundancy among microbial systems. Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen, and nitrate. However, the composition of functional genes was only weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the variations in B12 biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between the chlorophyll a concentration and B12 biosynthesis, confirming its importance in primary production in the global ocean. The results of this study reveal an essential ecological mechanism governing the assembly of microbes in nature: the environment selects for function rather than taxonomy; functional redundancy underlies stochastic community assembly.
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Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| | - Wei Qin
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
| | - Xinda Lu
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
DermBiont Inc.BostonMassachusettsUSA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - David Stahl
- Department of Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Nianzhi Jiao
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Institute of Marine Microbes and EcospheresXiamen UniversityXiamenChina
| | - Jizhong Zhou
- School of Biological SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- Institute for Environmental Genomics, University of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental Sciences, University of OklahomaNormanOklahomaUSA
- School of Computer Sciences, University of OklahomaNormanOklahomaUSA
| | - Jihua Liu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
| | - Qichao Tu
- Institute of Marine Science and TechnologyShandong UniversityQingdaoChina
- Joint Lab for Ocean Research and Education at Dalhousie UniversityShandong University and Xiamen UniversityQingdaoChina
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Moreno-Cabezuelo JÁ, Del Carmen Muñoz-Marín M, López-Lozano A, Athayde D, Simón-García A, Díez J, Archer M, Issoglio FM, García-Fernández JM. Production, homology modeling and mutagenesis studies on GlcH glucose transporter from Prochlorococcus sp. strain SS120. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148954. [PMID: 36563737 DOI: 10.1016/j.bbabio.2022.148954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The marine cyanobacterium Prochlorococcus is one of the main primary producers on Earth, which can take up glucose by using the high affinity, multiphasic transporter GlcH. We report here the overexpression of glcH from Prochlorococcus marinus strain SS120 in Escherichia coli. Modeling studies of GlcH using the homologous MelB melibiose transporter from Salmonella enterica serovar Typhimurium showed high conservation at the overall fold. We observed that an important structural interaction, mediated by a strong hydrogen bond between D8 and R141, is conserved in Prochlorococcus, although the corresponding amino acids in MelB from Salmonella are different. Biased docking studies suggested that when glucose reaches the pocket of the transporter and interacts with D8 and R141, the hydrogen bond network in which these residues are involved could be disrupted, favoring a conformational change with the subsequent translocation of the glucose molecule towards the cytoplasmic region of the pmGlcH structure. Based on these theoretical predictions and on the conservation of N117 and W348 in other MelB structures, D8, N117, R141 and W348 were mutated to glycine residues. Their key role in glucose transport was evaluated by glucose uptake assays. N117G and W348G mutations led to 17 % decrease in glucose uptake, while D8G and R141G decreased the glucose transport by 66 % and 92 % respectively. Overall, our studies provide insights into the Prochlorococcus 3D-structure of GlcH, paving the way for further analysis to understand the features which are involved in the high affinity and multiphasic kinetics of this transporter.
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Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - María Del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Ana Simón-García
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Federico M Issoglio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina.
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain.
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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:microorganisms11020455. [PMID: 36838420 PMCID: PMC9964548 DOI: 10.3390/microorganisms11020455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Department of Biology, University of Padua, 35100 Padua, Italy
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Natha, QLD 4111, Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Correspondence:
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Tychonema sp. BBK16 Characterisation: Lifestyle, Phylogeny and Related Phages. Viruses 2023; 15:v15020442. [PMID: 36851656 PMCID: PMC9958718 DOI: 10.3390/v15020442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Cyanobacterial expansion is harmful to the environment, the ecology of Lake Baikal and the economy of nearby regions and can be dangerous to people and animals. Since 2011, the process of colonisation of the lake with potentially toxic cyanobacteria belonging to the genus Tychonema has continued. An understanding of the mechanism of successful expansion of Tychonema requires scrutiny of biological and genomic features. Tychonema sp. BBK16 was isolated from the coastal zone of Lake Baikal. The morphology of BBK16 biofilm was studied with light, scanning electron and confocal microscopy. The biofilm is based on filaments of cyanobacteria, which are intertwined like felt; there are also dense fascicles of rope-like twisted filaments that impart heterogeneity to the surface of the biofilm. Genome sequencing, intergenomic comparisons and phylogenetic analyses indicated that Tychonema sp. BBK16 represent a new species related to planktic cyanobacterium Tychonema bourrellyi, isolated from Alpine lentic freshwater. Genome investigation revealed the genes possibly responsible for the mixotrophic lifestyle. The presence of CRISPR-Cas and restriction modification defence mechanisms allowed to suggest the existence of phages infecting Tychonema sp. BBK16. Analysis of CRISPR spacers and prophage-derived regions allowed to suggest related cyanophages. Genomic analysis supported the assumption that mobile elements and horizontal transfer participate in shaping the Tychonema sp. BBK16 genome. The findings of the current research suggest that the aptitude of Tychonema sp. BBK16 for biofilm formation and, possibly, its mixotrophic lifestyle provide adaptation advantages that lead to the successful expansion of this cyanobacterium in the Baikal's conditions of freshwater lake environments.
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Moreno-Cabezuelo JÁ, Gómez-Baena G, Díez J, García-Fernández JM. Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus. Microbiol Spectr 2023; 11:e0327522. [PMID: 36722960 PMCID: PMC10100731 DOI: 10.1128/spectrum.03275-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/29/2022] [Indexed: 02/02/2023] Open
Abstract
We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria. IMPORTANCE Glucose uptake by marine picocyanobacteria has been previously described and strongly suggests they are mixotrophic organisms (capable of using energy from the sun to make organic matter, but also to directly use organic matter from the environment when available). However, a detailed analysis of the effects of glucose addition on the proteome and metabolome of these microorganisms had not been carried out. Here, we analyzed three Prochlorococcus sp. and three Synechococcus sp. strains which were representative of several marine picocyanobacterial clades. We observed differential features in the effects of glucose availability, depending on both the genus and strain; our study illuminated the strategies utilized by these organisms to metabolize glucose and showed unexpected links to other pathways, such as circadian regulation. Furthermore, we found glucose addition had profound effects in the microbiome, favoring the growth of coexisting heterotrophic bacteria.
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Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - Guadalupe Gómez-Baena
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular-Campus de Excelencia Agroalimentaria CEIA3, Universidad de Córdoba, Cordoba, Spain
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Díez J, López-Lozano A, Domínguez-Martín MA, Gómez-Baena G, Muñoz-Marín MC, Melero-Rubio Y, García-Fernández JM. Regulatory and metabolic adaptations in the nitrogen assimilation of marine picocyanobacteria. FEMS Microbiol Rev 2023; 47:6794272. [PMID: 36323406 DOI: 10.1093/femsre/fuac043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Prochlorococcus and Synechococcus are the two most abundant photosynthetic organisms on Earth, with a strong influence on the biogeochemical carbon and nitrogen cycles. Early reports demonstrated the streamlining of regulatory mechanisms in nitrogen metabolism and the removal of genes not strictly essential. The availability of a large series of genomes, and the utilization of latest generation molecular techniques have allowed elucidating the main mechanisms developed by marine picocyanobacteria to adapt to the environments where they thrive, with a particular interest in the strains inhabiting oligotrophic oceans. Given that nitrogen is often limited in those environments, a series of studies have explored the strategies utilized by Prochlorococcus and Synechococcus to exploit the low concentrations of nitrogen-containing molecules available in large areas of the oceans. These strategies include the reduction in the GC and the cellular protein contents; the utilization of truncated proteins; a reduced average amount of N in the proteome; the development of metabolic mechanisms to perceive and utilize nanomolar nitrate concentrations; and the reduced responsiveness of key molecular regulatory systems such as NtcA to 2-oxoglutarate. These findings are in sharp contrast with the large body of knowledge obtained in freshwater cyanobacteria. We will outline the main discoveries, stressing their relevance to the ecological success of these important microorganisms.
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Affiliation(s)
- J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - Y Melero-Rubio
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba,14001, Spain
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Evseev P, Lukianova A, Tarakanov R, Tokmakova A, Popova A, Kulikov E, Shneider M, Ignatov A, Miroshnikov K. Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages. Int J Mol Sci 2023; 24:ijms24021586. [PMID: 36675099 PMCID: PMC9862828 DOI: 10.3390/ijms24021586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Rashit Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology National Research University, Institutskiy Per, 9, 141701 Dolgoprudny, Russia
| | - Anastasia Popova
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Eugene Kulikov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology National Research University, Institutskiy Per, 9, 141701 Dolgoprudny, Russia
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prosp. 60-letia Oktyabrya, 7-2, 117312 Moscow, Russia
| | - Mikhail Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
| | - Alexander Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, Russia
- Correspondence: (P.E.); (K.M.)
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Lindberg P, Kenkel A, Bühler K. Introduction to Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:1-24. [PMID: 37009973 DOI: 10.1007/10_2023_217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Cyanobacteria are highly interesting microbes with the capacity for oxygenic photosynthesis. They fulfill an important purpose in nature but are also potent biocatalysts. This chapter gives a brief overview of this diverse phylum and shortly addresses the functions these organisms have in the natural ecosystems. Further, it introduces the main topics covered in this volume, which is dealing with the development and application of cyanobacteria as solar cell factories for the production of chemicals including potential fuels. We discuss cyanobacteria as industrial workhorses, present established chassis strains, and give an overview of the current target products. Genetic engineering strategies aiming at the photosynthetic efficiency as well as approaches to optimize carbon fluxes are summarized. Finally, main cultivation strategies are sketched.
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Affiliation(s)
- Pia Lindberg
- Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Amelie Kenkel
- Helmholtzcenter for Environmental Research, Leipzig, Germany
| | - Katja Bühler
- Helmholtzcenter for Environmental Research, Leipzig, Germany.
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10
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Cabello-Yeves PJ, Callieri C, Picazo A, Schallenberg L, Huber P, Roda-Garcia JJ, Bartosiewicz M, Belykh OI, Tikhonova IV, Torcello-Requena A, De Prado PM, Puxty RJ, Millard AD, Camacho A, Rodriguez-Valera F, Scanlan DJ. Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates. BMC Biol 2022; 20:175. [PMID: 35941649 PMCID: PMC9361551 DOI: 10.1186/s12915-022-01379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. RESULTS Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. CONCLUSIONS The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain.
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980, Paterna, Valencia, Spain
| | | | - Paula Huber
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Av. Intendente Marino Km 8,200, (7130) Chascomús, Buenos Aires, Argentina.,Instituto Nacional de Limnología (INALI), CONICET-UNL, Ciudad Universitaria - Paraje el Pozo s/n, (3000), Santa Fé, Argentina
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain
| | - Maciej Bartosiewicz
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Olga I Belykh
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | - Irina V Tikhonova
- Limnological Institute, Russian Academy of Sciences, P.O. Box 278, 664033, Irkutsk, Russia
| | | | | | - Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, E-46980, Paterna, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain.,Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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11
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Abstract
Microbial communities have essential roles in ocean ecology and planetary health. Microbes participate in nutrient cycles, remove huge quantities of carbon dioxide from the air and support ocean food webs. The taxonomic and functional diversity of the global ocean microbiome has been revealed by technological advances in sampling, DNA sequencing and bioinformatics. A better understanding of the ocean microbiome could underpin strategies to address environmental and societal challenges, including achievement of multiple Sustainable Development Goals way beyond SDG 14 'life below water'. We propose a set of priorities for understanding and protecting the ocean microbiome, which include delineating interactions between microbiota, sustainably applying resources from oceanic microorganisms and creating policy- and funder-friendly ocean education resources, and discuss how to achieve these ambitious goals.
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12
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Selão TT. Exploring cyanobacterial diversity for sustainable biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3057-3071. [PMID: 35467729 DOI: 10.1093/jxb/erac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.
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Affiliation(s)
- Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
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13
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Mallén-Ponce MJ, Huertas MJ, Florencio FJ. Exploring the Diversity of the Thioredoxin Systems in Cyanobacteria. Antioxidants (Basel) 2022; 11:antiox11040654. [PMID: 35453339 PMCID: PMC9025218 DOI: 10.3390/antiox11040654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 02/04/2023] Open
Abstract
Cyanobacteria evolved the ability to perform oxygenic photosynthesis using light energy to reduce CO2 from electrons extracted from water and form nutrients. These organisms also developed light-dependent redox regulation through the Trx system, formed by thioredoxins (Trxs) and thioredoxin reductases (TRs). Trxs are thiol-disulfide oxidoreductases that serve as reducing substrates for target enzymes involved in numerous processes such as photosynthetic CO2 fixation and stress responses. We focus on the evolutionary diversity of Trx systems in cyanobacteria and discuss their phylogenetic relationships. The study shows that most cyanobacteria contain at least one copy of each identified Trx, and TrxA is the only one present in all genomes analyzed. Ferredoxin thioredoxin reductase (FTR) is present in all groups except Gloeobacter and Prochlorococcus, where there is a ferredoxin flavin-thioredoxin reductase (FFTR). Our data suggest that both TRs may have coexisted in ancestral cyanobacteria together with other evolutionarily related proteins such as NTRC or DDOR, probably used against oxidative stress. Phylogenetic studies indicate that they have different evolutionary histories. As cyanobacteria diversified to occupy new habitats, some of these proteins were gradually lost in some groups. Finally, we also review the physiological relevance of redox regulation in cyanobacteria through the study of target enzymes.
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Affiliation(s)
- Manuel J. Mallén-Ponce
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, 41092 Sevilla, Spain;
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Profesor García González s/n, 41012 Sevilla, Spain
- Correspondence: (M.J.M.-P.); (M.J.H.)
| | - María José Huertas
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, 41092 Sevilla, Spain;
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Profesor García González s/n, 41012 Sevilla, Spain
- Correspondence: (M.J.M.-P.); (M.J.H.)
| | - Francisco J. Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Américo Vespucio 49, 41092 Sevilla, Spain;
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Profesor García González s/n, 41012 Sevilla, Spain
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14
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Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220. Sci Rep 2022; 12:4805. [PMID: 35314715 PMCID: PMC8938411 DOI: 10.1038/s41598-022-08459-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Paradigms of metabolic strategies employed by photoautotrophic marine picocyanobacteria have been challenged in recent years. Based on genomic annotations, picocyanobacteria are predicted to assimilate organic nutrients via ATP-binding cassette importers, a process mediated by substrate-binding proteins. We report the functional characterisation of a modified sugar-binding protein, MsBP, from a marine Synechococcus strain, MITS9220. Ligand screening of MsBP shows a specific affinity for zinc (KD ~ 1.3 μM) and a preference for phosphate-modified sugars, such as fructose-1,6-biphosphate, in the presence of zinc (KD ~ 5.8 μM). Our crystal structures of apo MsBP (no zinc or substrate-bound) and Zn-MsBP (with zinc-bound) show that the presence of zinc induces structural differences, leading to a partially-closed substrate-binding cavity. The Zn-MsBP structure also sequesters several sulphate ions from the crystallisation condition, including two in the binding cleft, appropriately placed to mimic the orientation of adducts of a biphosphate hexose. Combined with a previously unseen positively charged binding cleft in our two structures and our binding affinity data, these observations highlight novel molecular variations on the sugar-binding SBP scaffold. Our findings lend further evidence to a proposed sugar acquisition mechanism in picocyanobacteria alluding to a mixotrophic strategy within these ubiquitous photosynthetic bacteria.
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15
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Chakdar H, Thapa S, Srivastava A, Shukla P. Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127609. [PMID: 34772552 DOI: 10.1016/j.jhazmat.2021.127609] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.
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Affiliation(s)
- Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, ID 47907-2048, United States
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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16
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Ford BA, Sullivan GJ, Moore L, Varkey D, Zhu H, Ostrowski M, Mabbutt BC, Paulsen IT, Shah BS. Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria. Biochem Soc Trans 2021; 49:2465-2481. [PMID: 34882230 PMCID: PMC8786288 DOI: 10.1042/bst20200244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/03/2021] [Accepted: 11/16/2021] [Indexed: 12/05/2022]
Abstract
Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
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Affiliation(s)
- Benjamin A. Ford
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Lisa Moore
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Deepa Varkey
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Hannah Zhu
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Martin Ostrowski
- Climate Change Cluster (C3), University of Technology Sydney, Sydney, Australia
| | - Bridget C. Mabbutt
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bhumika S. Shah
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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17
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Shuwang X, Sun J, Wei Y, Guo C. Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton. BIOLOGY 2021; 10:biology10121280. [PMID: 34943195 PMCID: PMC8698306 DOI: 10.3390/biology10121280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton-especially picoeukaryotic phytoplankton-in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2-0.6, 0.6-1.2, and 1.2-2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.
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Affiliation(s)
- Xinze Shuwang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqiu Wei
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
| | - Congcong Guo
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; (X.S.); (C.G.)
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18
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Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle. mSystems 2021; 6:e0094421. [PMID: 34609172 PMCID: PMC8547437 DOI: 10.1128/msystems.00944-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism, and biogeography within the SAR116 clade. This increased genomic diversity has led to the discovery of two subclades that, despite coexisting in the same environment, display different properties in their genomic makeup. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlined features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp), and strong purifying selection (low ratio of nonsynonymous to synonymous polymorphisms [dN/dS]). Besides, they were more abundant in metagenomic databases recruiting at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in metagenome-assembled genomes (MAGs), included the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way both clades can metabolize dimethylsulfoniopropionate (DMSP). IMPORTANCE The SAR116 clade of Alphaproteobacteria is a ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study these kinds of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genomic makeup of the two subclades that could serve to illustrate how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.
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19
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Nandagopal P, Steven AN, Chan LW, Rahmat Z, Jamaluddin H, Mohd Noh NI. Bioactive Metabolites Produced by Cyanobacteria for Growth Adaptation and Their Pharmacological Properties. BIOLOGY 2021; 10:1061. [PMID: 34681158 PMCID: PMC8533319 DOI: 10.3390/biology10101061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 02/08/2023]
Abstract
Cyanobacteria are the most abundant oxygenic photosynthetic organisms inhabiting various ecosystems on earth. As with all other photosynthetic organisms, cyanobacteria release oxygen as a byproduct during photosynthesis. In fact, some cyanobacterial species are involved in the global nitrogen cycles by fixing atmospheric nitrogen. Environmental factors influence the dynamic, physiological characteristics, and metabolic profiles of cyanobacteria, which results in their great adaptation ability to survive in diverse ecosystems. The evolution of these primitive bacteria resulted from the unique settings of photosynthetic machineries and the production of bioactive compounds. Specifically, bioactive compounds play roles as regulators to provide protection against extrinsic factors and act as intracellular signaling molecules to promote colonization. In addition to the roles of bioactive metabolites as indole alkaloids, terpenoids, mycosporine-like amino acids, non-ribosomal peptides, polyketides, ribosomal peptides, phenolic acid, flavonoids, vitamins, and antimetabolites for cyanobacterial survival in numerous habitats, which is the focus of this review, the bioactivities of these compounds for the treatment of various diseases are also discussed.
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Affiliation(s)
- Pavitra Nandagopal
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
| | - Anthony Nyangson Steven
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia;
| | - Liong-Wai Chan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
| | - Zaidah Rahmat
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Malaysia
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
| | - Nur Izzati Mohd Noh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Malaysia; (P.N.); (L.-W.C.); (Z.R.); (H.J.)
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20
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- R, Mondal S, Pathak J, Singh PR, Singh SP, Sinha RP. Computational Studies on Photolyase (Phr) Proteins of Cyanobacteria. Can J Microbiol 2021; 68:111-137. [PMID: 34587467 DOI: 10.1139/cjm-2021-0167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Photolyases (Phrs) are enzymes that utilize blue/ultraviolet (UV-A) region of light for repairing UV-induced cyclopyramidine dimer. We have studied Phr groups by bioinformatic analyses as well as active-site and structural modeling. The analysis of 238 amino acid sequences from 85 completely sequenced cyanobacterial genomes revealed five classes of Phrs, i.e., CPD Gr I, 6-4 Phrs/cryptochrome, Cry-DASH, Fe-S bacteria Phrs, and a group having fewer number of amino acids (276-385) in length. Distribution of Phr groups in cyanobacteria belonging to the order Synechococcales was found to be influenced by the habitats of the organisms. Class V Phrs were exclusively present in cyanobacteria. Unique motif and binding sites were reported in Group II and III. Fe-S protein binding site was only present in Group V. Active site residues and putative CPD/6-4pp binding residues are charged amino acids which were present on the surface of the proteins. Majority of hydrophilic amino acid residues were present on surface of Phrs. Sequence analysis confirmed the diverse nature of Phrs, though, sequence diversity does not affect their overall 3D structure. Protein-ligand interaction analysis identified novel CPD/6-4PP binding sites on Phrs. This structural information of Phrs can be used for the preparation of efficient Phr based formulations.
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Affiliation(s)
- Rajneesh -
- Banaras Hindu University Faculty of Science, 163931, Varanasi, Uttar Pradesh, India;
| | - Soumila Mondal
- Banaras Hindu University Faculty of Science, 163931, Varanasi, Uttar Pradesh, India;
| | - Jainendra Pathak
- Pt Jawaharlal Nehru College (Affiliated to Bundelkhand University Jhansi), Department of Botany, Banda, India;
| | - Prashant R Singh
- Banaras Hindu University Faculty of Science, 163931, Varanasi, Uttar Pradesh, India;
| | - Shailendra P Singh
- Banaras Hindu University Faculty of Science, 163931, Varanasi, Uttar Pradesh, India;
| | - Rajeshwar P Sinha
- Banaras Hindu University Faculty of Science, 163931, Varanasi, India, 221005;
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21
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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22
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Rozum JC, Gómez Tejeda Zañudo J, Gan X, Deritei D, Albert R. Parity and time reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks. SCIENCE ADVANCES 2021; 7:7/29/eabf8124. [PMID: 34272246 PMCID: PMC8284893 DOI: 10.1126/sciadv.abf8124] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/03/2021] [Indexed: 05/14/2023]
Abstract
We present new applications of parity inversion and time reversal to the emergence of complex behavior from simple dynamical rules in stochastic discrete models. Our parity-based encoding of causal relationships and time-reversal construction efficiently reveal discrete analogs of stable and unstable manifolds. We demonstrate their predictive power by studying decision-making in systems biology and statistical physics models. These applications underpin a novel attractor identification algorithm implemented for Boolean networks under stochastic dynamics. Its speed enables resolving a long-standing open question of how attractor count in critical random Boolean networks scales with network size and whether the scaling matches biological observations. Via 80-fold improvement in probed network size (N = 16,384), we find the unexpectedly low scaling exponent of 0.12 ± 0.05, approximately one-tenth the analytical upper bound. We demonstrate a general principle: A system's relationship to its time reversal and state-space inversion constrains its repertoire of emergent behaviors.
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Affiliation(s)
- Jordan C Rozum
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Jorge Gómez Tejeda Zañudo
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Xiao Gan
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dávid Deritei
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Réka Albert
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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23
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Lhee D, Lee J, Ettahi K, Cho CH, Ha JS, Chan YF, Zelzion U, Stephens TG, Price DC, Gabr A, Nowack ECM, Bhattacharya D, Yoon HS. Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis. Mol Biol Evol 2021; 38:344-357. [PMID: 32790833 PMCID: PMC7826189 DOI: 10.1093/molbev/msaa206] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic photosynthetic organelles, plastids, are the powerhouses of many aquatic and terrestrial ecosystems. The canonical plastid in algae and plants originated >1 Ga and therefore offers limited insights into the initial stages of organelle evolution. To address this issue, we focus here on the photosynthetic amoeba Paulinella micropora strain KR01 (hereafter, KR01) that underwent a more recent (∼124 Ma) primary endosymbiosis, resulting in a photosynthetic organelle termed the chromatophore. Analysis of genomic and transcriptomic data resulted in a high-quality draft assembly of size 707 Mb and 32,361 predicted gene models. A total of 291 chromatophore-targeted proteins were predicted in silico, 208 of which comprise the ancestral organelle proteome in photosynthetic Paulinella species with functions, among others, in nucleotide metabolism and oxidative stress response. Gene coexpression analysis identified networks containing known high light stress response genes as well as a variety of genes of unknown function (“dark” genes). We characterized diurnally rhythmic genes in this species and found that over 49% are dark. It was recently hypothesized that large double-stranded DNA viruses may have driven gene transfer to the nucleus in Paulinella and facilitated endosymbiosis. Our analyses do not support this idea, but rather suggest that these viruses in the KR01 and closely related P. micropora MYN1 genomes resulted from a more recent invasion.
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Affiliation(s)
- Duckhyun Lhee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, Korea
| | - Khaoula Ettahi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji-San Ha
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ya-Fan Chan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ
| | - Udi Zelzion
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ
| | - Dana C Price
- Department of Entomology, Center for Vector Biology, Rutgers University, New Brunswick, NJ
| | - Arwa Gabr
- Microbiology and Molecular Genetics Graduate Program, Rutgers University, New Brunswick, NJ
| | - Eva C M Nowack
- Institut für Mikrobielle Zellbiologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | | | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling. PLoS Comput Biol 2021; 17:e1008983. [PMID: 33961619 PMCID: PMC8143392 DOI: 10.1371/journal.pcbi.1008983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/24/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
Marine nitrogen-fixing microorganisms are an important source of fixed nitrogen in oceanic ecosystems. The colonial cyanobacterium Trichodesmium and diatom symbionts were thought to be the primary contributors to oceanic N2 fixation until the discovery of the unusual uncultivated symbiotic cyanobacterium UCYN-A (Candidatus Atelocyanobacterium thalassa). UCYN-A has atypical metabolic characteristics lacking the oxygen-evolving photosystem II, the tricarboxylic acid cycle, the carbon-fixation enzyme RuBisCo and de novo biosynthetic pathways for a number of amino acids and nucleotides. Therefore, it is obligately symbiotic with its single-celled haptophyte algal host. UCYN-A receives fixed carbon from its host and returns fixed nitrogen, but further insights into this symbiosis are precluded by both UCYN-A and its host being uncultured. In order to investigate how this syntrophy is coordinated, we reconstructed bottom-up genome-scale metabolic models of UCYN-A and its algal partner to explore possible trophic scenarios, focusing on nitrogen fixation and biomass synthesis. Since both partners are uncultivated and only the genome sequence of UCYN-A is available, we used the phylogenetically related Chrysochromulina tobin as a proxy for the host. Through the use of flux balance analysis (FBA), we determined the minimal set of metabolites and biochemical functions that must be shared between the two organisms to ensure viability and growth. We quantitatively investigated the metabolic characteristics that facilitate daytime N2 fixation in UCYN-A and possible oxygen-scavenging mechanisms needed to create an anaerobic environment to allow nitrogenase to function. This is the first application of an FBA framework to examine the tight metabolic coupling between uncultivated microbes in marine symbiotic communities and provides a roadmap for future efforts focusing on such specialized systems. Reduction of dinitrogen gas to biologically useful forms via nitrogen fixation is a key component of the biogeochemical cycle. In the marine environment, the cyanobacteria UCYN-A (Candidatus Atelocyanobacterium thalassa) has been found to be a primary contributor to biological nitrogen fixation at a global scale. UCYN-A exhibits a highly streamlined genome which lacks genes coding for essential cyanobacterial processes such as the energy-generating TCA cycle, oxygen-producing photosystem II, the carbon-fixing RuBisCo and de novo production pathways for numerous amino acids and nucleotides. Thus, it exists in a symbiosis with unicellular planktonic algae where it exchanges fixed nitrogen for fixed carbon with its host. However, both UCYN-A and its symbiotic partner remain uncultured under laboratory conditions. This necessitates implementing a computational approach to glean insights into UCYN-A’s unique physiology and metabolic processes governing the symbiotic association. To this end, we develop a constraints-based framework that infers all possible trophic scenarios consistent with the observed data. Possible mechanisms employed by UCYN-A to accommodate diazotrophy with daytime carbon fixation by the host (i.e., two mutually incompatible processes) are also elucidated. We envision that the developed framework using UCYN-A and its algal host will be used as a roadmap and motivate the study of similarly unique microbial systems in the future.
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Wright RJ, Erni-Cassola G, Zadjelovic V, Latva M, Christie-Oleza JA. Marine Plastic Debris: A New Surface for Microbial Colonization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11657-11672. [PMID: 32886491 DOI: 10.1021/acs.est.0c02305] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plastics become rapidly colonized by microbes when released into marine environments. This microbial community-the Plastisphere-has recently sparked a multitude of scientific inquiries and generated a breadth of knowledge, which we bring together in this review. Besides providing a better understanding of community composition and biofilm development in marine ecosystems, we critically discuss current research on plastic biodegradation and the identification of potentially pathogenic "hitchhikers" in the Plastisphere. The Plastisphere is at the interface between the plastic and its surrounding milieu, and thus drives every interaction that this synthetic material has with its environment, from ecotoxicity and new links in marine food webs to the fate of the plastics in the water column. We conclude that research so far has not shown Plastisphere communities to starkly differ from microbial communities on other inert surfaces, which is particularly true for mature biofilm assemblages. Furthermore, despite progress that has been made in this field, we recognize that it is time to take research on plastic-Plastisphere-environment interactions a step further by identifying present gaps in our knowledge and offering our perspective on key aspects to be addressed by future studies: (I) better physical characterization of marine biofilms, (II) inclusion of relevant controls, (III) study of different successional stages, (IV) use of environmentally relevant concentrations of biofouled microplastics, and (V) prioritization of gaining a mechanistic and functional understanding of Plastisphere communities.
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Affiliation(s)
- Robyn J Wright
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Gabriel Erni-Cassola
- Man-Society-Environment (MSE) program, University of Basel, Basel 4003, Switzerland
| | - Vinko Zadjelovic
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Mira Latva
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Joseph A Christie-Oleza
- University of the Balearic Islands, Palma 07122, Spain
- IMEDEA (CSIC-UIB), Esporles 07190, Spain
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Tschoeke D, Salazar VW, Vidal L, Campeão M, Swings J, Thompson F, Thompson C. Unlocking the Genomic Taxonomy of the Prochlorococcus Collective. MICROBIAL ECOLOGY 2020; 80:546-558. [PMID: 32468160 DOI: 10.1007/s00248-020-01526-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.
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Affiliation(s)
- Diogo Tschoeke
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Vinicius W Salazar
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Livia Vidal
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Mariana Campeão
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Jean Swings
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
- Laboratory of Microbiology, Ghent University, Gent, Belgium
| | - Fabiano Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Cristiane Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil.
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Gabr A, Grossman AR, Bhattacharya D. Paulinella, a model for understanding plastid primary endosymbiosis. JOURNAL OF PHYCOLOGY 2020; 56:837-843. [PMID: 32289879 PMCID: PMC7734844 DOI: 10.1111/jpy.13003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/07/2023]
Abstract
The uptake and conversion of a free-living cyanobacterium into a photosynthetic organelle by the single-celled Archaeplastida ancestor helped transform the biosphere from low to high oxygen. There are two documented, independent cases of plastid primary endosymbiosis. The first is the well-studied instance in Archaeplastida that occurred ca. 1.6 billion years ago, whereas the second occurred 90-140 million years ago, establishing a permanent photosynthetic compartment (the chromatophore) in amoebae in the genus Paulinella. Here, we briefly summarize knowledge about plastid origin in the Archaeplastida and then focus on Paulinella. In particular, we describe features of the Paulinella chromatophore that make it a model for examining earlier events in the evolution of photosynthetic organelles. Our review stresses recently gained insights into the evolution of chromatophore and nuclear encoded DNA sequences in Paulinella, metabolic connectivity between the endosymbiont and cytoplasm, and systems that target proteins into the chromatophore. We also describe future work with Paulinella, and the potential rewards and challenges associated with developing further this model system.
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Affiliation(s)
- Arwa Gabr
- School of Graduate Studies, Graduate Program in Molecular Bioscience and Program in Microbiology and Molecular Genetics, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, California 94305, USA
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Abstract
The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats compared to eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious traits that serve as the raw materials for genetic innovation.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Marian L Schmidt
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
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Accumulation of ambient phosphate into the periplasm of marine bacteria is proton motive force dependent. Nat Commun 2020; 11:2642. [PMID: 32457313 PMCID: PMC7250820 DOI: 10.1038/s41467-020-16428-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteria acquire phosphate (Pi) by maintaining a periplasmic concentration below environmental levels. We recently described an extracellular Pi buffer which appears to counteract the gradient required for Pi diffusion. Here, we demonstrate that various treatments to outer membrane (OM) constituents do not affect the buffered Pi because bacteria accumulate Pi in the periplasm, from which it can be removed hypo-osmotically. The periplasmic Pi can be gradually imported into the cytoplasm by ATP-powered transport, however, the proton motive force (PMF) is not required to keep Pi in the periplasm. In contrast, the accumulation of Pi into the periplasm across the OM is PMF-dependent and can be enhanced by light energy. Because the conventional mechanism of Pi-specific transport cannot explain Pi accumulation in the periplasm we propose that periplasmic Pi anions pair with chemiosmotic cations of the PMF and millions of accumulated Pi pairs could influence the periplasmic osmolarity of marine bacteria. The ubiquitous oceanic bacteria harbour an external phosphate buffer for modulating phosphate (Pi) uptake. Here, using both oceanic SAR11, Prochlorococcus and Synechococcus strains as a model, the authors show that the Pi buffer accumulation in the periplasm is proton motive force-dependent and can be enhanced by light energy.
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Muñoz-Marín MC, Gómez-Baena G, López-Lozano A, Moreno-Cabezuelo JA, Díez J, García-Fernández JM. Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus. THE ISME JOURNAL 2020; 14:1065-1073. [PMID: 32034281 PMCID: PMC7174365 DOI: 10.1038/s41396-020-0603-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/23/2022]
Abstract
Marine picocyanobacteria of the Prochlorococcus and Synechococcus genera have been longtime considered as autotrophic organisms. However, compelling evidence published over the last 15 years shows that these organisms can use different organic compounds containing key elements to survive in oligotrophic oceans, such as N (amino acids, amino sugars), S (dimethylsulfoniopropionate, DMSP), or P (ATP). Furthermore, marine picocyanobacteria can also take up glucose and use it as a source of carbon and energy, despite the fact that this compound is devoid of limiting elements and can also be synthesized by using standard metabolic pathways. This review will outline the main findings suggesting mixotrophy in the marine picocyanobacteria Prochlorococcus and Synechococcus, and its ecological relevance for these important primary producers.
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Affiliation(s)
- M C Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - G Gómez-Baena
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - A López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J A Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - J M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, planta 1, ala Este, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
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31
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Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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Khumalo MJ, Nzuza N, Padayachee T, Chen W, Yu JH, Nelson DR, Syed K. Comprehensive Analyses of Cytochrome P450 Monooxygenases and Secondary Metabolite Biosynthetic Gene Clusters in Cyanobacteria. Int J Mol Sci 2020; 21:ijms21020656. [PMID: 31963856 PMCID: PMC7014017 DOI: 10.3390/ijms21020656] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
The prokaryotic phylum Cyanobacteria are some of the oldest known photosynthetic organisms responsible for the oxygenation of the earth. Cyanobacterial species have been recognised as a prosperous source of bioactive secondary metabolites with antibacterial, antiviral, antifungal and/or anticancer activities. Cytochrome P450 monooxygenases (CYPs/P450s) contribute to the production and diversity of various secondary metabolites. To better understand the metabolic potential of cyanobacterial species, we have carried out comprehensive analyses of P450s, predicted secondary metabolite biosynthetic gene clusters (BGCs), and P450s located in secondary metabolite BGCs. Analysis of the genomes of 114 cyanobacterial species identified 341 P450s in 88 species, belonging to 36 families and 79 subfamilies. In total, 770 secondary metabolite BGCs were found in 103 cyanobacterial species. Only 8% of P450s were found to be part of BGCs. Comparative analyses with other bacteria Bacillus, Streptomyces and mycobacterial species have revealed a lower number of P450s and BGCs and a percentage of P450s forming part of BGCs in cyanobacterial species. A mathematical formula presented in this study revealed that cyanobacterial species have the highest gene-cluster diversity percentage compared to Bacillus and mycobacterial species, indicating that these diverse gene clusters are destined to produce different types of secondary metabolites. The study provides fundamental knowledge of P450s and those associated with secondary metabolism in cyanobacterial species, which may illuminate their value for the pharmaceutical and cosmetics industries.
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Affiliation(s)
- Makhosazana Jabulile Khumalo
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (M.J.K.); (N.N.); (T.P.)
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (M.J.K.); (N.N.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (M.J.K.); (N.N.); (T.P.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (M.J.K.); (N.N.); (T.P.)
- Correspondence: (D.R.N.); (K.S.)
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Lawrence TJ, Amrine KCH, Swingley WD, Ardell DH. tRNA functional signatures classify plastids as late-branching cyanobacteria. BMC Evol Biol 2019; 19:224. [PMID: 31818253 PMCID: PMC6902448 DOI: 10.1186/s12862-019-1552-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/29/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Eukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data. RESULTS Using Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data. CONCLUSIONS Phylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies.
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Affiliation(s)
- Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831 USA
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
| | - Katherine CH Amrine
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
- Insight Data Science, 500 3rd St., San Francisco, CA, 94107 USA
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, 1425 Lincoln Hwy., DeKalb, IL, 60115 USA
| | - David H Ardell
- Quantitative and Systems Biology Program, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
- Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Rd., Merced, CA, 95343 USA
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Complete genome sequence and comparative analysis of Streptomyces seoulensis, a pioneer strain of nickel superoxide dismutase. Genes Genomics 2019; 42:273-281. [PMID: 31797314 DOI: 10.1007/s13258-019-00878-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Streptomyces seoulensis has contributed to the discovery and initiation of extensive research into nickel superoxide dismutase (NiSOD), a unique type of superoxide dismutase found in actinomycetes. Still so far, there is no information about whole genome sequence of this strain. OBJECTIVE To investigate complete genome sequence and perform bioinformatic analyses for genomic functions related with nickel-associated genes. METHODS DNA was extracted using the Wizard Genomic DNA Purification Kit then sequenced using a Pacific Biosciences SMRT cell 8Pac V3 DNA Polymerase Binding Kit P6 with the PacBiov2 RSII platform. We assembled the PacBio long-reads with the HGAP3 pipeline. RESULTS We obtained complete genome sequence of S. seoulensis, which comprises a 6,339,363 bp linear chromosome. While analyzing the genome to annotate the genomic function, we discovered the nickel-associated genes. We observed that the sodN gene encoding for NiSOD is located adjacent to the sodX gene, which encodes for the nickel-type superoxide dismutase maturation protease. In addition, several nickel-associated genes and gene clusters-nickel-responsive regulator, nickel uptake transporter, nickel-iron [NiFe]-hydrogenase and other putative genes were also detected. Strain specific genes were discovered through a comparative analysis of S. coelicolor and S. griseus. Further bioinformatic analyses revealed that this strain encodes at least 22 putative biosynthetic gene clusters, thereby implying that S. seoulensis has the potential to produce novel bioactive compounds. CONCLUSION We annotated the genome and determined nickel-associated genes and gene clusters and discovered biosynthetic gene clusters for secondary metabolites implying that S. seoulensis produces novel types of bioactive compounds.
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Flores-Uribe J, Philosof A, Sharon I, Fridman S, Larom S, Béjà O. A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus 'relic' prophage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:598-604. [PMID: 31125500 DOI: 10.1111/1758-2229.12773] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, a genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here, we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.
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Affiliation(s)
- José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91106, USA
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel
- Tel Hai College, Upper Galilee, 12210, Israel
| | - Svetlana Fridman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Shirley Larom
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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Mishra LS, Mielke K, Wagner R, Funk C. Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2173-2184. [PMID: 30721974 PMCID: PMC6460958 DOI: 10.1093/jxb/erz004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 05/20/2023]
Abstract
FtsH (filamentation-temperature-sensitive protein H) proteases are a family of membrane-bound enzymes present in eubacteria, animals, and plants. Besides the 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis, there are five genes coding for members that are assumed to be proteolytically inactive due to mutations in the protease domain; these are termed FtsHi (i for inactive). Despite their lack of proteolytic activity, these FtsHi members seem to be important for chloroplast and plant development as four out of five homozygous knockout-mutants of FtsHis are embryo-lethal. Here, we analysed the Darwinian fitness of weak homozygous (ftshi1,3,4) and heterozygous (ftshi/FTSHi2,4,5) mutants. We compared the growth and development of these mutants to their respective wild-type Arabidopsis plants under controlled laboratory conditions and in the field, and we also evaluated the photosynthetic efficiency by pulse-amplitude modulation fluorescence. Homologous genotypes were subjected to various stress conditions in a greenhouse and gene co-expression as well as phylogenetic analyses were performed. Analysis of the gene-expression network of the five FTSHi genes indicated common clusters with genes encoding FtsH12, OTP51, and methylase. Phylogenetic analyses pointed to a common evolution (and common disappearance in grasses and gymnosperms) of FtsH12 and multiple presumably proteolytically inactive FtsHi enzymes. Our data show that the FtsHi enzymes are highly important during the seedling stage and for Darwinian fitness analyses in semi-natural conditions.
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Affiliation(s)
| | - Kati Mielke
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Raik Wagner
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Christiane Funk
- Department of Chemistry, Umeå University, Umeå, Sweden
- Correspondence:
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Abstract
Next-generation sequencing (NGS) has been used to determine the reference sequences of model organisms. This allows us to identify mutations by the chromosome number and sequence position where the base sequence has been altered, independent of any phenotypic alteration. Because the re-sequencing method by NGS covers all of the genome, it enables detection of the small number of spontaneous de novo germline mutations that occur in the reproductive lineage. The spontaneous mutation rate varies depending on the environment; for example, it increases when 8-oxoguanine accumulates. If the mutation rate (per replication) is greater than 1/genome size (2n), at least one mutation would generally occur in each cell division on average, producing cells with a different genome from the parent cell. Organisms with larger genomes and more divisions by cells in the reproductive lineage are expected to show higher mutation rates per generation, if the mutation rate per replication is constant among species. The accumulation of mutations that arose in the genome of ancestor cells has resulted in heterogeneity and diversity among extant species. In this sense, the ability to produce mutations in cells of the reproductive lineage can be considered as a key feature of organisms, even if mutations also present an unavoidable risk.
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Affiliation(s)
- Kunihiko Sakumi
- Division of Neurofunctional Genomics, Medical Institute of Bioregulation, Kyushu University
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Noack S, Baumgart M. Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction. Trends Biotechnol 2019; 37:126-139. [DOI: 10.1016/j.tibtech.2018.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022]
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Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes ( mpeBA and cpeBA). Front Microbiol 2019; 10:45. [PMID: 30761097 PMCID: PMC6363710 DOI: 10.3389/fmicb.2019.00045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.
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Affiliation(s)
| | - Giorgio Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrea Di Cesare
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
- Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Cristiana Callieri
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
| | - Nathan A. M. Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
- The Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
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Moreno-Cabezuelo JÁ, López-Lozano A, Díez J, García-Fernández JM. Differential expression of the glucose transporter gene glcH in response to glucose and light in marine picocyanobacteria. PeerJ 2019; 6:e6248. [PMID: 30648008 PMCID: PMC6330958 DOI: 10.7717/peerj.6248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/09/2018] [Indexed: 11/20/2022] Open
Abstract
Background Our team discovered that Prochlorococcus can take up glucose, in a process that changes the transcriptional pattern of several genes involved in glucose metabolization. We have also shown that glcH encodes a very high affinity glucose transporter, and that glucose is taken up by natural Prochlorococcus populations. We demonstrated that the kinetic parameters of glucose uptake show significant diversity in different Prochlorococcus and Synechococcus strains. Here, we tested whether the transcriptional response of glcH to several glucose concentrations and light conditions was also different depending on the studied strain. Methods Cultures were grown in the light, supplemented with five different glucose concentrations or subjected to darkness, and cells harvested after 24 h of treatment. qRT-PCR was used to determine glcH expression in four Prochlorococcus and two Synechococcus strains. Results In all studied strains glcH was expressed in the absence of glucose, and it increased upon glucose addition to cultures. The changes differed depending on the strain, both in the magnitude and in the way cells responded to the tested glucose concentrations. Unlike the other strains, Synechococcus BL107 showed the maximum glucose uptake at 5 nM glucose. Darkness induced a strong decrease in glcH expression, especially remarkable in Prochlorococcus MIT9313. Discussion Our results suggest that marine picocyanobacteria are actively monitoring the availability of glucose, to upregulate glcH expression in order to exploit the presence of sugars in the environment. The diverse responses observed in different strains suggest that the transcriptional regulation of glucose uptake has been adjusted by evolutive selection. Darkness promotes a strong decrease in glcH expression in all studied strains, which fits with previous results on glucose uptake in Prochlorococcus. Overall, this work reinforces the importance of mixotrophy for marine picocyanobacteria.
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Affiliation(s)
- José Ángel Moreno-Cabezuelo
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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Barrera-Rojas J, de la Vara LG, Ríos-Castro E, Leyva-Castillo LE, Gómez-Lojero C. The distribution of divinyl chlorophylls a and b and the presence of ferredoxin-NADP + reductase in Prochlorococcus marinus MIT9313 thylakoid membranes. Heliyon 2018; 4:e01100. [PMID: 30627680 PMCID: PMC6312871 DOI: 10.1016/j.heliyon.2018.e01100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/22/2018] [Accepted: 12/24/2018] [Indexed: 12/12/2022] Open
Abstract
The marine unicellular green cyanobacterium Prochlorococcus marinus MIT9313 belongs to the most abundant and photosynthetically productive genus of cyanobacteria in the oceans. This monophyletic genus use divinyl chlorophyll a (Chl a 2 ) and b (Chl b 2 ) to build the photosystems and the membrane-intrinsic Pcb-type antennae. We used the mild detergent n-dodecyl β D-maltopyranoside to solubilize the thylakoid membranes. Gel electrophoresis and sucrose gradient ultracentrifugation was then used to separate the complexes of the photosynthetic apparatus. The proteins and the pigments were identified by mass spectrometry. Protein complexes were characterized biochemically, and the distribution of Chl a 2 and Chl b 2 was determined. The photosynthetic apparatus was shown as supercomplexes formed by Photosystem II dimers with up to eight PcbB proteins; Photosystem I was present as trimers. A heterogeneous distribution of pigments was shown using sucrose gradient-enriched fractions with ratios of [Chl b 2 ]/[Chl a 2 ] of 2.16 ± 0.13, 1.86 ± 0.08, and 2.61 ± 0.07, for Photosystem I, Photosystem II, and PcbB, respectively. These ratios of Chl b/a are without precedent in organisms with oxygenic photosynthesis. Diaphorase activity was measured in the fractions of the sucrose gradient. Gel electrophoresis, immunodetection, and mass spectrometry were used to conclude that the commonly soluble protein ferredoxin-NADP+ reductase (FNR) is a membrane-anchored protein (probably associated to cytochrome b 6 f complex) in the low-light adapted Prochlorococcus marinus MIT9313.
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Affiliation(s)
- Jesús Barrera-Rojas
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Mexico
| | | | | | | | - Carlos Gómez-Lojero
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Mexico
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Genome Rearrangement Shapes Prochlorococcus Ecological Adaptation. Appl Environ Microbiol 2018; 84:AEM.01178-18. [PMID: 29915114 PMCID: PMC6102989 DOI: 10.1128/aem.01178-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/10/2018] [Indexed: 12/13/2022] Open
Abstract
Prochlorococcus, the most abundant and smallest known free-living photosynthetic microorganism, plays a key role in marine ecosystems and biogeochemical cycles. Prochlorococcus genome evolution is a fundamental issue related to how Prochlorococcus clades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted the Prochlorococcus genome evolution from the perspective of genome structure and associated the genome rearrangement with the Prochlorococcus clade differentiation and subsequent ecological adaptation. Prochlorococcus is the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles. Prochlorococcus can be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted clade I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructed Prochlorococcus evolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role in Prochlorococcus evolution. We also found that the Prochlorococcus clades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations. IMPORTANCEProchlorococcus, the most abundant and smallest known free-living photosynthetic microorganism, plays a key role in marine ecosystems and biogeochemical cycles. Prochlorococcus genome evolution is a fundamental issue related to how Prochlorococcus clades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted the Prochlorococcus genome evolution from the perspective of genome structure and associated the genome rearrangement with the Prochlorococcus clade differentiation and subsequent ecological adaptation.
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Chew J, Leypunskiy E, Lin J, Murugan A, Rust MJ. High protein copy number is required to suppress stochasticity in the cyanobacterial circadian clock. Nat Commun 2018; 9:3004. [PMID: 30068980 PMCID: PMC6070526 DOI: 10.1038/s41467-018-05109-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/12/2018] [Indexed: 11/09/2022] Open
Abstract
Circadian clocks generate reliable ~24-h rhythms despite being based on stochastic biochemical reactions. The circadian clock in Synechococcus elongatus uses a post-translational oscillator that cycles deterministically in a test tube. Because the volume of a single bacterial cell is much smaller than a macroscopic reaction, we asked how clocks in single cells function reliably. Here, we show that S. elongatus cells must express many thousands of copies of Kai proteins to effectively suppress timing errors. Stochastic modeling shows that this requirement stems from noise amplification in the post-translational feedback loop that sustains oscillations. The much smaller cyanobacterium Prochlorococcus expresses only hundreds of Kai protein copies and has a simpler, hourglass-like Kai system. We show that this timer strategy can outperform a free-running clock if internal noise is significant. This conclusion has implications for clock evolution and synthetic oscillator design, and it suggests hourglass-like behavior may be widespread in microbes. Circadian clocks must maintain their fidelity despite stochasticity arising from finite protein copy numbers. Here, the authors show that a small cyanobacterium relies on an environmentally driven timer likely because its low protein copy numbers cannot support an accurate free-running clock.
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Affiliation(s)
- Justin Chew
- Medical Scientist Training Program, Pritzker School of Medicine, University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
| | - Eugene Leypunskiy
- Graduate Program in Biophysical Sciences, University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
| | - Jenny Lin
- Department of Biochemistry and Molecular Biology, University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
| | - Arvind Murugan
- Department of Physics, University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
| | - Michael J Rust
- Department of Physics, University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA. .,Department of Molecular Genetics and Cell Biology, University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA.
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Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness. mSystems 2018; 3:mSystems00040-18. [PMID: 29854954 PMCID: PMC5974335 DOI: 10.1128/msystems.00040-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Microbes evolve within complex ecological communities where biotic interactions impact both individual cells and the environment as a whole. Here we examine how cellular regulation in the marine cyanobacterium Prochlorococcus is influenced by a heterotrophic bacterium, Alteromonas macleodii, under different light conditions. We monitored the transcriptome of Prochlorococcus, grown either alone or in coculture, across a diel light:dark cycle and under the stress of extended darkness-a condition that cells would experience when mixed below the ocean's euphotic zone. More Prochlorococcus transcripts exhibited 24-h periodic oscillations in coculture than in pure culture, both over the normal diel cycle and after the shift to extended darkness. This demonstrates that biotic interactions, and not just light, can affect timing mechanisms in Prochlorococcus, which lacks a self-sustaining circadian oscillator. The transcriptomes of replicate pure cultures of Prochlorococcus lost their synchrony within 5 h of extended darkness and reflected changes in stress responses and metabolic functions consistent with growth cessation. In contrast, when grown with Alteromonas, replicate Prochlorococcus transcriptomes tracked each other for at least 13 h in the dark and showed signs of continued biosynthetic and metabolic activity. The transcriptome patterns suggest that the heterotroph may be providing energy or essential biosynthetic substrates to Prochlorococcus in the form of organic compounds, sustaining this autotroph when it is deprived of solar energy. Our findings reveal conditions where mixotrophic metabolism may benefit marine cyanobacteria and highlight new impacts of community interactions on basic Prochlorococcus cellular processes. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on the planet. These cells play a central role in the physiology of surrounding heterotrophs by supplying them with fixed organic carbon. It is becoming increasingly clear, however, that interactions with heterotrophs can affect autotrophs as well. Here we show that such interactions have a marked impact on the response of Prochlorococcus to the stress of extended periods of darkness, as reflected in transcriptional dynamics. These data suggest that diel transcriptional rhythms within Prochlorococcus, which are generally considered to be strictly under the control of light quantity, quality, and timing, can also be influenced by biotic interactions. Together, these findings provide new insights into the importance of microbial interactions on Prochlorococcus physiology and reveal conditions where heterotroph-derived compounds may support autotrophs-contrary to the canonical autotroph-to-heterotroph trophic paradigm.
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Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
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Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. The future of genomics in polar and alpine cyanobacteria. FEMS Microbiol Ecol 2018; 94:4904125. [PMID: 29506259 PMCID: PMC5939894 DOI: 10.1093/femsec/fiy032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/23/2018] [Indexed: 01/01/2023] Open
Abstract
In recent years, genomic analyses have arisen as an exciting way of investigating the functional capacity and environmental adaptations of numerous micro-organisms of global relevance, including cyanobacteria. In the extreme cold of Arctic, Antarctic and alpine environments, cyanobacteria are of fundamental ecological importance as primary producers and ecosystem engineers. While their role in biogeochemical cycles is well appreciated, little is known about the genomic makeup of polar and alpine cyanobacteria. In this article, we present ways that genomic techniques might be used to further our understanding of cyanobacteria in cold environments in terms of their evolution and ecology. Existing examples from other environments (e.g. marine/hot springs) are used to discuss how methods developed there might be used to investigate specific questions in the cryosphere. Phylogenomics, comparative genomics and population genomics are identified as methods for understanding the evolution and biogeography of polar and alpine cyanobacteria. Transcriptomics will allow us to investigate gene expression under extreme environmental conditions, and metagenomics can be used to complement tradition amplicon-based methods of community profiling. Finally, new techniques such as single cell genomics and metagenome assembled genomes will also help to expand our understanding of polar and alpine cyanobacteria that cannot readily be cultured.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
| | - Patricia Sánchez-Baracaldo
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
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Domínguez-Martín MA, López-Lozano A, Clavería-Gimeno R, Velázquez-Campoy A, Seidel G, Burkovski A, Díez J, García-Fernández JM. Differential NtcA Responsiveness to 2-Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus. Front Microbiol 2018; 8:2641. [PMID: 29375510 PMCID: PMC5767323 DOI: 10.3389/fmicb.2017.02641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022] Open
Abstract
Previous studies showed differences in the regulatory response to C/N balance in Prochlorococcus with respect to other cyanobacteria, but no information was available about its causes, or the ecological advantages conferred to thrive in oligotrophic environments. We addressed the changes in key enzymes (glutamine synthetase, isocitrate dehydrogenase) and the ntcA gene (the global nitrogen regulator) involved in C/N metabolism and its regulation, in three model Prochlorococcus strains: MED4, SS120, and MIT9313. We observed a remarkable level of diversity in their response to azaserine, a glutamate synthase inhibitor which increases the concentration of the key metabolite 2-oxoglutarate, used to sense the C/N balance by cyanobacteria. Besides, we studied the binding between the global nitrogen regulator (NtcA) and the promoter of the glnA gene in the same Prochlorococcus strains, and its dependence on the 2-oxoglutarate concentration, by using isothermal titration calorimetry, surface plasmon resonance, and electrophoretic mobility shift. Our results show a reduction in the responsiveness of NtcA to 2-oxoglutarate in Prochlorococcus, especially in the MED4 and SS120 strains. This suggests a trend to streamline the regulation of C/N metabolism in late-branching Prochlorococcus strains (MED4 and SS120), in adaptation to the rather stable conditions found in the oligotrophic ocean gyres where this microorganism is most abundant.
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Affiliation(s)
- María A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Rafael Clavería-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas, Barcelona, Spain.,Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - Gerald Seidel
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Burkovski
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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48
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Cheng J, Lu H, Li K, Zhu Y, Zhou J. Enhancing growth-relevant metabolic pathways of Arthrospira platensis (CYA-1) with gamma irradiation from 60Co. RSC Adv 2018; 8:16824-16833. [PMID: 35540541 PMCID: PMC9080328 DOI: 10.1039/c8ra01626g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/01/2018] [Indexed: 11/21/2022] Open
Abstract
The biomass yield of Arthrospira mutant ZJU9000 was 176% higher than that of wild type on day 4, and the results of transcriptome sequencing showed that processes related to cell growth were synergistically enhanced in this mutant. The amount of energy for biomass accumulation increased because the efficiency of the photoreaction was enhanced by the elevated levels of chlorophyll a and carotene. The increased biosynthesis rates of ribose phosphate, nucleotides and multiple vitamins increased the production of genetic materials for cell proliferation. Furthermore, the carbon concentration mechanism in mutant ZJU9000 was enhanced, indicating the increased utilization efficiency of CO2 at low concentration (0.04 vol% in air). The enhancement of these growth-relevant metabolic pathways contributed to the robust growth of Arthrospira mutant ZJU9000. Growth-relevant metabolic pathways of Arthrospira enhanced after gamma irradiation.![]()
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Affiliation(s)
- Jun Cheng
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Hongxiang Lu
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Ke Li
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Yanxia Zhu
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Junhu Zhou
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
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49
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Pittayakanchit W, Lu Z, Chew J, Rust MJ, Murugan A. Biophysical clocks face a trade-off between internal and external noise resistance. eLife 2018; 7:37624. [PMID: 29988019 PMCID: PMC6059770 DOI: 10.7554/elife.37624] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/23/2018] [Indexed: 01/27/2023] Open
Abstract
Many organisms use free running circadian clocks to anticipate the day night cycle. However, others organisms use simple stimulus-response strategies ('hourglass clocks') and it is not clear when such strategies are sufficient or even preferable to free running clocks. Here, we find that free running clocks, such as those found in the cyanobacterium Synechococcus elongatus and humans, can efficiently project out light intensity fluctuations due to weather patterns ('external noise') by exploiting their limit cycle attractor. However, such limit cycles are necessarily vulnerable to 'internal noise'. Hence, at sufficiently high internal noise, point attractor-based 'hourglass' clocks, such as those found in a smaller cyanobacterium with low protein copy number, Prochlorococcus marinus, can outperform free running clocks. By interpolating between these two regimes in a diverse range of oscillators drawn from across biology, we demonstrate biochemical clock architectures that are best suited to different relative strengths of external and internal noise.
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Affiliation(s)
- Weerapat Pittayakanchit
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States
| | - Zhiyue Lu
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States
| | - Justin Chew
- Medical Scientist Training Program, Pritzker School of MedicineUniversity of ChicagoChicagoUnited States
| | - Michael J Rust
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States,Department of Molecular Genetics and Cell BiologyUniversity of ChicagoChicagoUnited States
| | - Arvind Murugan
- Department of PhysicsUniversity of ChicagoChicagoUnited States,The James Franck InstituteUniversity of ChicagoChicagoUnited States
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50
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Guéguen L, Duret L. Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition. Mol Biol Evol 2017; 35:734-742. [PMID: 29220511 PMCID: PMC5850866 DOI: 10.1093/molbev/msx308] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The measurement of synonymous and nonsynonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation probabilities of nonsynonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS, or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process. In many clades, this assumption of stationarity is in fact incorrect, and we show here through simulations and analyses of empirical data that nonstationarity biases the estimate of dN, dS, and ω. We show that the bias in the estimate of ω can be fixed by explicitly taking into consideration nonstationarity in the modeling of codon evolution, in a maximum likelihood framework. Moreover, we propose an exact method for estimating dN and dS on branches, based on stochastic mapping, that can take into account nonstationarity. This method can be directly applied to any kind of codon evolution model, as long as neutrality is clearly parameterized.
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Affiliation(s)
- Laurent Guéguen
- Laboratoire de Biologie et Biométrie Évolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1-Université de Lyon, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biologie et Biométrie Évolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1-Université de Lyon, Villeurbanne, France
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